file 10 - R code for simulated bottleneck in the N=10 x1 population

This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x1 population. Once the bottleneck is simulated, only the allele frequencies are used to generate the subsequent pedigree so variance in individual IBD generated during the bottleneck is not retained. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17 and files 23 – 27.